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Was the e. coli sensitive to the doxycycline or the new antibiotic based on the culture results?
How long was he on this new antibiotic for? Has he had a follow-up scrotal ultrasound? Has he been taking any NSAIDS like ibuprofen?
OK. It sounds like they are doing the correct things for him. It sounds to me like he may either have a residual testicle infection that may need more antibiotics, or this may just be residual pain from the recent infection. The ibuprofen should help stop the pain from the inflammation. The ultrasound and a repeat urine culture will help to rule out persistent infection. Hope this helps.